Markers + reference

Ligusticopsis

14 species · Apiaceae · Apiales

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Species 14
Genome length 147–149 kb
Candidate markers 258
Primer pairs 50

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

2 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhB Genome 2215 0.1479 0.88 64.3 yes View details
ndhB Genome 2215 0.1479 0.88 64.3 yes View details
trnH-GUG-psbA Genome 215 0.0332 0.95 78.1 yes View details
ycf2-ndhB Genome 1417 0.0567 0.76 72.2 yes View details
ndhB-trnH-GUG Genome 1999 0.0387 0.83 66.5 no View details
rps4-trnT-UGU Genome 367 0.0103 0.95 64.7 yes View details
trnL-CAA-rps7 Genome 485 0.0705 0.73 64.2 yes View details
petA-psbJ Genome 926 0.0038 0.99 63.9 yes View details
ycf1-ndhF Genome 47 0.0996 0.57 63.7 yes View details
rps7-trnL-CAA Genome 485 0.0578 0.72 63.7 yes View details
ndhC-trnV-UAC Genome 1087 0.0067 1.00 62.8 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 50 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 255–288 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 305–338 1.000 87.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 319–352 1.000 87.4
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 318–351 1.000 87.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 320–353 1.000 87.4
rps4-trnT-UGU_p1 rps4-trnT-UGU AGATCACTTCCGGCTCTAGG CTCAGAGGTTAGAGCATCGC 505–532 1.000 83.0
rps4-trnT-UGU_p2 rps4-trnT-UGU GTTAGTCCCGGTAAAGCTCC CTCAGAGGTTAGAGCATCGC 475–502 1.000 83.0
rps4-trnT-UGU_p3 rps4-trnT-UGU AGATCACTTCCGGCTCTAGG ATGGTCATCGGTTCGATTCC 473–500 1.000 82.3
rps4-trnT-UGU_p4 rps4-trnT-UGU GTTAGTCCCGGTAAAGCTCC ATGGTCATCGGTTCGATTCC 443–470 1.000 82.3
rps4-trnT-UGU_p5 rps4-trnT-UGU TTTTTGAAACGAGGTCCCCG CTCAGAGGTTAGAGCATCGC 442–469 1.000 80.1
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCAGGCCCTTTGTTAATCGG CCGAGAAAGTCTACGGTTCG 1227–1262 1.000 81.2
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TAATCGGGGCTAAAACTCCG CCGAGAAAGTCTACGGTTCG 1214–1249 1.000 77.3
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCAGGCCCTTTGTTAATCGG GTTCGAGTCCGTATAGCCCT 1212–1247 1.000 76.6
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CCCTTTGTTAATCGGGGCTA CCGAGAAAGTCTACGGTTCG 1222–1257 1.000 76.4
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GGGGCTAAAACTCCGGAAAC CCGAGAAAGTCTACGGTTCG 1209–1244 1.000 75.6
petA-psbJ_p1 petA-psbJ CTTACGTGTCCAAGGCCTTT GCTGGTATTCTTGTGATCGGT 979–1138 1.000 75.4
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTGGC GCTGGTATTCTTGTGATCGGT 966–1125 1.000 75.0
petA-psbJ_p3 petA-psbJ CTTACGTGTCCAAGGCCTTT AGCTGGTATTCTTGTGATCGG 980–1139 1.000 74.7
petA-psbJ_p4 petA-psbJ GGCCTTTTGTTCTTCTTGGC AGCTGGTATTCTTGTGATCGG 967–1126 1.000 74.3
petA-psbJ_p5 petA-psbJ GATCCCTTACGTGTCCAAGG GCTGGTATTCTTGTGATCGGT 984–1143 1.000 73.8
ycf2-ndhB_p1 ycf2-ndhB CAGCCCTTTGTCTCTGTGTT ATCACGGGTTCTTCTCTCCA 1729–2033 0.214 54.0
ycf2-ndhB_p2 ycf2-ndhB CAGCCCTTTGTCTCTGTGTT TCACGGGTTCTTCTCTCCAT 1728–2032 0.214 54.0
ycf2-ndhB_p3 ycf2-ndhB GTTCTTGCAGAGTGGAACCA ATCACGGGTTCTTCTCTCCA 1853–2157 0.214 53.9
ycf2-ndhB_p4 ycf2-ndhB GTTCTTGCAGAGTGGAACCA TCACGGGTTCTTCTCTCCAT 1852–2156 0.214 53.9
ycf2-ndhB_p5 ycf2-ndhB GGCAAGCGGATCCTTTATGA TCACGGGTTCTTCTCTCCAT 1905–2209 0.214 53.8
ndhB_p1 ndhB GTTGCGGAAGAACGGACTAT AAGCCCAAAGAGGTGAATGG 2736–2874 0.214 51.9
ndhB_p2 ndhB GTTGCGGAAGAACGGACTAT ATATAGGCCCGAGTTGGACA 2855–2993 0.214 51.5
ndhB_p3 ndhB GTTGCGGAAGAACGGACTAT TATAGGCCCGAGTTGGACAT 2854–2992 0.214 51.5
ndhB_p4 ndhB TAGCCGGAAAGTTATGTGGC AAGCCCAAAGAGGTGAATGG 2766 0.143 44.9
ndhB_p5 ndhB TAGCCGGAAAGTTATGTGGC TATAGGCCCGAGTTGGACAT 2884 0.143 44.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Ligusticopsis acaulis NC_064322.1 148509 View on NCBI ↗
Ligusticopsis brachyloba NC_063838.1 148163 View on NCBI ↗
Ligusticopsis capillacea NC_049051.1 147808 View on NCBI ↗
Ligusticopsis daucoides NC_063845.1 148078 View on NCBI ↗
Ligusticopsis hispida NC_049053.1 147797 View on NCBI ↗
Ligusticopsis involucrata NC_049054.1 147752 View on NCBI ↗
Ligusticopsis likiangensis NC_049055.1 148196 View on NCBI ↗
Ligusticopsis litangensis OP899836.1 147482 View on NCBI ↗
Ligusticopsis miyiensis NC_085243.1 148076 View on NCBI ↗
Ligusticopsis modesta NC_065500.1 148133 View on NCBI ↗
Ligusticopsis multivittata NC_071794.1 148262 View on NCBI ↗
Ligusticopsis rechingeriana NC_065482.1 148525 View on NCBI ↗
Ligusticopsis scapiformis NC_049057.1 148107 View on NCBI ↗
Ligusticopsis wallichiana NC_065501.1 148594 View on NCBI ↗